The invention relates to a method for the quantitative determination of DNA sequences containing at least one mutationally eliminated restriction site in which the PCR-technology is applied.
The study of the formation and processing of chromosomal damage is of fundamental importance to many aspects of the life sciences including evolution, hereditary disease, carcinogenesis and possibly aging. Mutations in the form of deletions, insertions, rearrangements and base pair substitutions are hereditary consequences of spontaneous processes and the exposure to DNA damaging agents. Since mutation rates at low or no toxicity are in the range of 10xe2x88x925 to 10xe2x88x928 (for an average size target gene) the isolation of a mutated cell requires the selection of an altered phenotype. In most cases cells are isolated which have acquired the ability to grow in the presence of a particular drug. In all systems using phenotypic selection only mutations are recovered which have resulted in a selectable change in the function of the target protein or in its elimination altogether. This represents a severe limitation since many mutations remain functionally silent. Furthermore, only a few genes are suitable targets for drug selection. Drug resistance can be the consequence of a missense mutation or small in-frame deletion/insertion which renders the target protein inert to drug toxicity (e.g. resistance to cuabain). More useful are non-essential target genes/proteins which upon inactivation allow cell growth in the presence of a particular selecting drug because a wider spectrum of mutations can be obtained under these conditions. Target genes in this second category are X-linked hypoxanthineguanine-phosphoribosyl transferase (hgprt), bacterial xanthine-guanine-phosphoribosyl transferase (gpt), chromosomally integrated into hgprt 3  mammalian cells and adenine-phosphoribosyl transferase (aprt): hgprt and gpt-mutants are selectable with 6-thioguanine (6-TG) and aprt-mutants with 8-azaadenine (8-aza-A). By simply measuring the frequency of the generation of drug-resistant phenotypes, preferably coupled with the demonstration of a loss in the activity of the target enzyme, overall mutation frequencies can be obtained albeit without any information regarding the molecular event by which they arose.
The sophisticated protocols using molecular cloning of target genes from drug-resistant cells furnished insights into mutagenic mechanisms first in bacteria and then in mammalian cells over the last decade. Considerable progress was made with the help of shuttle vectors which allow the rescue of an extrachromosomal plasmid from mammalian cells, its amplification in bacteria and finally its sequencing by standard methodology. While important information has been gathered with this approach it has several serious disadvantages (e.g. the presence of variable numbers of copies of the vector per cell and its extrachromosomal location do not allow conclusions about the role of local chromosome- and DNA-structure on lesion-processing in mutagenesis). Work with bona fide shuttle vectors has been reviewed (Banbury Report 28 xe2x80x9cMammalian Mutagenesisxe2x80x9d (1987); see in Friedberg and Hanawalt, eds. xe2x80x9cMechanisms and Consequences of DNA Damage Processingxe2x80x9d (1989)) and is not further discussed.
An advanced shuttle vector system has been developed by Davidson et al. (Ashman and Davidson, (1987); Davidson et al. (1988); Greenspan et al. (1988)) who constructed a hgprtxe2x88x92 L-cell line with a chromosomally integrated bacterial gpt-gene (as part of a vector containing an SV40 origin). Cells mutated in the gpt-gene are selectable with 6-TG, the plasmid can be rescued and amplified by fusion with COS cells and then sequenced. Limitations of this system are relatively high spontaneous mutation frequencies ( greater than 10xe2x88x925) and the formation of gross rearrangements during vector recovery which necessitates the isolation of a. xe2x80x9cmajority plasmidxe2x80x9d (with a xe2x80x9cnormalxe2x80x9d restriction pattern); advantageous is the good recovery of deletions. Of particular interest is the study of the reversion of specific gpt mutations induced by ethylmethanesulfonate (EMS). This ethylating agent which modifies preferentially guanine residues specifically reverts mutations which have resulted from Axe2x80xa2T xe2x86x92xe2x86x92xe2x86x92 greater than Gxe2x80xa2C transitions or Gxe2x80xa2Cxe2x86x92xe2x86x92xe2x86x92 greater than Cxe2x80xa2G transversions. Reversion frequencies with 3.3mM EMS of a specific bp were 1-4xc3x9710xe2x88x925 (Greenspan et al. (1986)).
An analogous approach has also been taken by Tindall and Stankowski (Stankowski and Tindall (1987); Tindall and Stankowski (1987)) who compared the mutability of a chromosomally integrated bacterial gpt-gene to that of the endogenous hgprt-gene in chinese hamster ovary (CHO) cells. Much higher mutability of gpt was noted for clastogens, possibly because the flanking sequences at the insertion site of the gpt-gene are non-essential for viability.
Meuth et al. selected spontaneous (Nalbantoglu et al. (1986); Nalbantoglu et al. (1987)) or radiation induced (Breimer et al. (1987)) aprt mutants (with 8-aza-A) from a CHO line which is hemizygous for this small gene (3.8 kb).
Either large deletions (detectable on Southern blots) or mutants which had gained or lost a restriction site (Southern/RFLP) were cloned and sequenced. Only relatively few mutations induced by ionizing radiation contained large deletions (6 out of 25); several deletions were flanked by direct repeats or at least one terminus was associated with a region of dyad symmetry. Spontaneous point mutations in aprt were mostly simple transitions and transversions. In contrast, ionizing radiation induced preferentially massive deletions in the hgprt-gene documenting locus specificity for mutations which are caused by the same mutagen.
An ingenious protocol for the analysis of 8-aza-A selected aprt mutants in CHO cells has been devised by Glickman et al.: Size-fractionated DNA is cloned into lambda which is then grown in a host containing a plasmid with flanking sequences of the hamster aprt-gene. This results in efficient recombinational transfer of the aprt-gene from lambda to the plasmid. The plasmid is rescued and sequenced using the M13 vector system. Spontaneous mutations were mostly Gxe2x80xa2Cxe2x86x92Axe2x80xa2T transitions. This could be due to cytosine deamination or reflect the fidelity of mammalian polymerases; all (except one) base-pair (bp) substitutions resulted in an amino acid change suggesting that protein structure and function co-determine the spectrum of mutants which are selected by 8-aza-A (De Jong et al. (1988)). Point mutations (i.e. no detectable changes on Southern blots because no relevant restriction sites were affected) induced by ionizing radiation were mostly simple transversions and transitions and small deletions. The latter were in some cases flanked by direct repeats (Grosovsky et al. (1988)). Ultraviolet light induced mutations were mostly targeted to dipyrimidine sites and consisted of Gxe2x80xa2Cxe2x86x92xe2x86x92Axe2x80xa2T transitions (Drobetsky et al. (1987)). Important general insights derive from this work. The fact that mutations in aprt were characteristic for a particular mutagen and distributed non-randomly points to a role for a chromatin/DNA xe2x80x9ccontextxe2x80x9d. xe2x80x9cMicro-environmentxe2x80x9d determines damage distribution, relative efficiency of error-free and error-prone repair, region- and site-specific repair, site specificity of polymerase fidelity, transcriptional activity etc. (Bohr et al. (1987)). However, mutation distribution in phenotypically selected systems is also affected by protein selectable sites and protein functional hot spots.
A breakthrough in mutagenesis research (and many other aspects of molecular biology) arrived with the introduction of the polymerase chain reaction (PCR) which allows the potent amplification of single copy genes (or their transcripts) in unfractionated cellular DNA or even in crude cell lysates (Saiki et al. (1988); Mullis and Fallona (1987) and EP-A1 201 184, EP-A2 200 362, and EP-A1 237 362). PCR was also used to amplify gpt sequences in 6-TG-resistant AS52 cells (i.e. hgprtxe2x88x92 CHO cells with one copy of chromosomally integrated bacterial gpt). The amplified material was analyzed by direct sequercing. 40-45% of the spontaneous mutations consisted of small deletions with a 3 bp deletion hot spot and point mutations (the remaining 55-60% were large deletions detectable on Southern blots). The proneness of the gpt-gene in AS52 for deletions may be a consequence of its insertion into repetitive sequences. (Note: Spontaneous gpt mutations in E. coli are mostly point mutations).
PCR has also been applied to the analysis of hgprt-mutations by Skopek et al. (Simpson et al. (1988)). Because of the large size of the hgprt-gene a cDNA copy was first produced from RNA with reverse transcriptase (RT). Regions of the hgprt-cDNA were amplified and cloned into M13 for sequencing by standard procedures. Three ethylnitrosourea (ENU) induced mutations consisted of an Axe2x80xa2Txe2x86x92Gxe2x80xa2C transition, an Axe2x80xa2Txe2x86x92Txe2x80xa2A transversion and an abnormal splice site (Vrieling et al. (1988)). A combination of PCR with denaturing gradient gel electrophoresis (DGGE) was applied by Thilly et al. for the analysis of hgprt-mutations in 6-TG selected human leucocytes (Cariello et al. (1988)). Hgprt-exon 3 was amplified by PCR connected to a GC-clamp and cleaved. Mutated exon 3 sequences were then separated from wild-type by DGGE. Mutated fragments were directly sequenced. Methyl-N-nitro-N-nitrosoguanidine (MNNG) and ICR 191 mutations were analyzed by this approach (Thilly, W., personal communication).
The ultimate goal remains the characterization of mutants in the intact animal rather than in cultured cells. Different cell types in a particular organ may differ in the metabolism of promutagens and in the processing of DNA lesions. Cell-cell interactions may affect mutagenic mechanisms. Only from in vivo mutation spectra in the human, safe conclusions can be reached concerning the type and concentrations of mutagens/carcinogens in our environment (Lohman et al. (1987); Delehanty (1986)). Ex vivo experiments with human T-lymphocytes have so far come closest to this goal. In a particular study 6-TG resistant T-cell clones from 8 donors were expanded in vitro with T-cell growth factor and major changes in the hgprt-gene were analyzed by Southern blotting. Approximately 10% of the 6-TG resistant clones had gross changes (Nicklas et al. (1986)). In a different approach by Mendelsohn et al., mutations in a cell surface protein are isolated by cell sorting (Delehanty et al. (1986)). Recently a shuttle vector system in transgenic mice has yielded first promising results for bona fide in vivo mutagenesis (Lohman et al. (1987)).
The isolation of spontaneous or xenobiotic-induced mutations at low toxicity represents a formidable taskxe2x80x94spontaneous mutation frequencies (per average size target gene) being in the range of 10xe2x88x928 (see e.g. Stankowski and Tindall (1987); Nalbantoglu et al. (1987); Nicklas et al. (1987)).
As discussed above, all presently available mammalian mutation systems require the isolation of cells which have acquired resistance to a selecting drug. This xe2x80x9cphenotypicxe2x80x9d selection is based either on the inactivation or activation, (resulting in decreased or increased drug resistance) of a particular target protein. Only a few genes can be used for this purposexe2x80x94usually hemizygous genes which are not directly relevant to human disease (hgprt represents an exception). Many DNA sequence changes remain silent since only mutations which impair protein function can be monitored (except mutations at splice sites). Because of the need for drug selection at best ex vivo experiments can be carried out, since drug selection in the animal/human is not feasible. Ideally then a human mutation system should be designed which allows the quantitative study of any target gene on the molecular level directly in tissue biopsies. This requires the replacement of biological by biochemical selection of mutated gene sequences or polypeptides.
Thus, the technical problem underlying the present invention is to provide a fast and reliable biochemical assay for the quantitative determination of mutated gene (DNA) sequences.
The solution of this technical problem is achieved by providing the embodiments characterized in the attached set of claims.
Accordingly, the present invention relates to a method for the quantitative determination of DNA sequences containing at least one mutationally eliminated restriction site, comprising the following steps:
(a) isolation of DNA from a sample;
(b) mixing a defined amount of DNA obtained in step (a) with a defined amount of a DNA sequence used as an internal standard (hereinafter referred to as xe2x80x9cstandard DNA sequencexe2x80x9d) which does not contain in a cleavable form the restriction site corresponding to said mutationally eliminated restriction site;
(c) complete cleavage of the mixture of DNA sequences obtained in step (a) with a least a restriction enzyme recognizing the restriction site corresponding to the wild-type DNA sequence but being mutationally eliminated in the DNA sequence to be quantitatively determined;
(d) size fractionation of the DNA fragments obtained in step (c) and isolation of a fraction of DNA fragments containing the DNA sequence to be quantitatively determined;
(e) amplification of said DNA sequence to be quantitatively determined and of the standard DNA sequence by a method comprising the steps of:
(ea) carrying out about 25-50 PCR cycles, preferably about 40 to 50 PCR cycles, most preferably 40 to 45 PCR cycles, wherein said DNA sequence to be quantitatively determined and said standard DNA sequence are selectively amplified during at least the initial 10 to 15 PCR cycles while continuously eliminating any residual wild-type DNA sequences, and
(eb) carrying out at least the last 3 PCR cycles, preferably at least the last 5 PCR cycles, and preferably not more than 10 PCR cycles with nested primers; and
(f) quantitative determination of the amount of said DNA sequence containing at least one mutationally eliminated restriction site by comparison with the amount of said standard DNA sequence in the DNA fragments obtained by the amplification in step (e).
The term xe2x80x9cimutationally eliminated restriction sitexe2x80x9d refers to a restriction site which occurs in the non-mutated wild-type DNA sequence of a given gene to be investigated, but which is eliminated by e.g. a point mutation in the mutated DNA sequence to be quantitatively determined. The PCR techniques applied in the method of the present invention are explained in detail e.g. in EP-A2 201 184. The term xe2x80x9cnested primerxe2x80x9d refers to primers which are complementary to sequences located towards the inside of a previously amplified fragment and, therefore, give rise to a shortened amplified DNA fragment.
The above method of the present invention is fast and reliable. It is of particular value because it permits the direct quantitative analysis of mutations in non-dividing human tissue explants, e.g. in biopsy samples or blood cell samples such as leucocytes. The method of the present invention can be applied to determine mutations in any gene of known structure, e.g. a proto-oncogene or a target gene for genetic disease in any organism. It can also be used to determine the level of background mutations in the general population. Furthermore, the method of the present invention can be applied in serial tests of potentially mutagenic or carcinogenic drugs in tissue cultures. In contrast to the present invention current bacterial and mammalian mutagenesis tests use target genes which are irrelevant to the etiology of cancer and genetic diseases. So far, the generally applied test for the determination of mutagenic or carcinogenic activities of a given drug is the Ames-test. However, this test suffers from the decisive disadvantage that it only is an indirect bacterial test and that laboratory animals have to be killed in order to obtain the necessary liver microsome fractions. Additionally, it has to be understood that none of the PCR-techniques known so far permitted a reliable quantitative analysis and determination of a low frequency of a mutated DNA sequence in the presence of a large excess of unaltered wild-type DNA. In existing methods wild-type and mutated sequences are coamplified and their relative frequencies remain unchanged in the amplification product. In addition, the low fidelity of Taq polymerase which is commonly used in PCR results in the introduction of artefactual mutations into the amplified sequences.
In a preferred embodiment the present invention relates to the above methods in which the quantitative determination in step (f) is effected by a dot blot hybridization in which probes are hybridized to a dilution series of the DNA fragments obtained by the amplification in step (e), said probes being specific for said DNA sequence to be quantitatively determined and for said standard DNA sequence.
Since the number of standard DNA molecules which had been added to genomic DNA at the outset is known, the frequency of a particular mutation can be estimated by comparison of the intensity of its signal on the dot blot with that of the standard.
In a further preferred embodiment of the method of the present invention the nested primers used in step (eb) carry restriction enzyme recognition sequences at their 51xe2x80x2-terminus, and the quantitative determination in step (f) is effected by carrying out the following additional steps:
(fa) preparation of recombinant vectors by cloning the DNA fragments obtained by the amplification in step (e) via their terminal restriction sites into a suitable vector;
(fb) transformation of host cells with the recombinant vectors obtained in step (fa);
(fc) cultivation of the transformed host cells obtained in step (fb) under suitable conditions;
(fd) quantitative determination of host cells in the culture which contain said DNA sequence to be quantitatively determined and of host cells in the culture which contain said standard DNA sequence, said determination being effected by hybridization with probes which are specific for said DNA sequence to be quantitatively determined and for said standard DNA sequence.
When effecting the cloning in step (fa), it may be necessary to cleave the vector and the PCR products with an appropriate restriction enzyme.
In a particularly preferred embodiment of the present invention the vector is a virulent bacteriophage and the determination in step (fd) is effected by plaque hybridization. Each individual bacteriophage plaque corresponds to a single type of mutation, to the standard DNA sequence, or to residual wild-type sequences. The frequency of each set of identified mutant plaques normalized by the frequency of standard plaques is a measure of relative mutation frequencies. Absolute mutation frequencies are obtained when the data is related to the amount of genomic DNA used in the test.
In a further particularly preferred embodiment of the present invention bacteriophages carrying the standard DNA sequence and/or bacteriophages carrying said DNA sequence to be quantitatively determined are used as (a) separate control(s). DNA sequences containing authentic mutations in the restriction site of choice can be synthesized in vitro, incorporated into a virulent bacteriophage and serve as positive controls for the selectivity of the plaque hybridization assay.
In another preferred embodiment the completeness of the cleavage in step (c) of the method of the present invention is ascertained by preparing a Southern Blot.
In a particularly preferred embodiment of the method of the present invention all amplification cycles in step (ea) are selectively eliminating any residual wild-type DNA sequences. The amplification product after each PCR cycle is restricted with an enzyme recognizing wild-type DNA which may have been synthesized on residual wild-type sequences still contained in the original sample. Since the amplified DNA fragment is usually short, e.g. about 200-350 base pairs and unmethylated, its digestion is particularly efficient.
In another particularly preferred embodiment of the method of the present invention the selective amplification continuously eliminating any residual wild-type DNA sequences is effected by using during each of the first 10-15 selective amplification cycles a restriction enzyme recognizing the restriction site corresponding to the wild-type DNA sequence but being mutationally eliminated in the DNA sequence to be quantitatively determined. A preferred restriction enzyme is the heat stable enzyme TaqI because it remains active during the PCR-cycles. Thus, in a particularly preferred embodiment of the present invention a combination of the enzymes Taq polymerase and TaqI is used. The selective elimination of wild-type DNA sequences is effected in this method independent of the methylation status of the DNA, since the PCR amplified DNA is usually not methylated.
In another preferred embodiment of the present invention said standard DNA sequence
(A) is identical to the DNA sequence to be quantitatively determined except for at least two alterations allowing the discrimination of the standard DNA sequence over said DNA sequence to be quantitatively determined;
(B) has the same amplification efficiency as said DNA sequences to be quantitatively determined.
The standard DNA sequence is in this embodiment in all aspects identical to wild type except for 2-3 base pair changes at the DNA sequence to be quantitated. Therefore, the efficiency of its amplification is equal to that of wild-type DNA or of a particular mutation. The fact that the standard DNA contains at least 2 base pair changes at the site allows its distinction from bona fide single base pair mutations in the final colony- or plaque hybridization assay.
In a particularly preferred embodiment of the present invention, said sequence alterations of said standard DNA sequence are located in said restriction site being mutationally eliminated.
In another particularly preferred embodiment of the present invention said nested primers used in step (eb) carry EcoRI recognition sequences at their 5xe2x80x2-terminus. Inclusion of EcoRI sequences at the 5xe2x80x2-ends of the nested primers allows the facile cloning of the amplification product into standard cloning vectors. Since EcoRI sites are only used on the nested primers during the last PCR cycles (step (eb)) only the final PCR products become clonable eliminating some undesirable amplification products which may have formed in earlier cycles.
In a further preferred embodiment of the present invention the data obtained in step (f) are confirmed by DNA sequence analysis. When virulent bacteriophages are used as cloning vectors, the individual resulting plaque only harbors a single specific cloned DNA sequence. The DNA content of individual plaques is recovered and the cloned DNA sequenced by standard procedures confirming the results of plaque hybridization.
In a particularly preferred embodiment of the method of the present invention the polymerase used for said about 10 to 15 initial PCR cycles is the T4- or T7-polymerase. It is advantageous to use the T4- or T7-polymerase instead of the Taq-polymerase because their inherent fidelity in the amplification reaction is superior to that of Taq-polymerase. This reduces the danger of producing artefactual changes in the sequence to be determined during PCR, especially if the original sample of restricted genomic DNA contained residual, undigested wild-type sequences.
After 10-15 initial PCR cycles of high fidelity the bona fide mutated sequences to be determined have been sufficiently enriched so that Taq-polymerase can be used in the subsequent PCR cycles.
In another preferred embodiment of the present invention, the DNA sequence containing at least one mutationally eliminated restriction site is at least a part of a cancer related gene, preferably an oncogene, or of a gene related to a hereditary disease.
There are several cases where a mutational event which is related to the etiology of a human disease is accompanied by the loss of a restriction enzyme recognition sequence. Important examples are the mutational activation of the protooncogene c-Ha-ras. Mutational alterations of the tumor suppressor gene p53, of a tumor gene involved in the origin of retinoblastoma, and of a gene located on chromosome 18 q responsible for certain forms of colorectal carcinoma are additional cases in point in carcinogenesis. The Hemophilia Factor VIII gene and the al-antitrypsin Z gene represent examples where a hereditary disease in man is caused by a single base pair mutation which results in the elimination of an enzyme recognition site.
In a particularly preferred embodiment of the present invention, the oncogene is the Ha-ras gene.
In a further particularly preferred embodiment of the present invention, the oncogene is the human c-Ha-ras gene.
In a further particularly preferred embodiment of the present invention the restriction site which is mutationally eliminated in the Ha-ras oncogene is the MspI site located at codon 12 of this gene. In this case the restriction enzyme used during the selective amplification cycles is MspI or any isoschizomer thereof.
In another particularly preferred embodiment of the present invention the restriction site which is mutationally eliminated in the Ha-ras oncogene is the TaqI site located at nucleotide positions 2508 to 2511 being part of codons for isoleucine and glutamine in exon 3 of this gene. In this case the restriction enzyme used during the selective amplification cycles is TaqI or any isoschizomer thereof. However, using the heat-stable enzyme TaqI is advantageous because it remains active throughout the PCR cycles.
It has to be understood that unless indicated otherwise any numbers referring to PCR cycles which have to be effected when applying the method of the present invention are approximate values only, which may not be interpreted as particularly limiting the scope of the present invention. The person skilled in the art will be able to also apply this method with similar values providing essentially the same results which are therefore also part of the present invention.